This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. # BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra. # Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. # Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. # qvality performs nonparametric estimation of posterior error probabilities. # Fido uses a probability model to rank proteins according to the posterior probability of their presence in a complex mixture, based on evidence derived from a shotgun proteomics experiment.